github nipreps/mriqc 26.1.0

2 hours ago
  • Docker: docker pull nipreps/mriqc:26.1.0 (linux/amd64 and linux/arm64)
  • PyPI: pip install mriqc==26.1.0 (Python 3.13 or newer)

The first minor release of the 26.x series.
MRIQC now supports FLAIR images, and a fix to the head mask changes the background IQMs of every anatomical run.

With thanks to @cooper-sharp for their first contribution (FLAIR support), to @celprov for the summary of the DWI report, and to @asaraog, @DimitriPapadopoulos, @jdotc1 and @jhlegarreta, whose pull requests and proposals some of the changes below build on.

Highlights

  • FLAIR images: *_FLAIR runs go through the anatomical workflow, which normalizes them to the T2w template, and get participant and group reports (#1438). FLAIR IQMs are not uploaded to the MRIQC Web API.
  • A head mask that keeps the brain: since 23.1.0, every head mask included the two outermost sagittal planes, and where the field of view cut the brain, the brain fell into the background (#1479).
  • BIDS inheritance: metadata set only in top-level sidecars (for example, RepetitionTime in task-rest_bold.json) now reaches the workflows (#1471).
  • DataLad in the container image: the image installs a working boto3 again, so runs on DataLad datasets no longer need --no-datalad-get (#1478).

Backward-incompatible changes

  • The background IQMs of every anatomical run change: summary_bg_*, snrd_*, fber and qi_2. On five T1w runs of ds007486, the median changes were +7% for fber, +1% for snrd_total and −28% for qi_2. Where the field of view cuts the brain, as in reduced-FoV FLAIR, they change much more, and so does cnr. Do not mix anatomical IQMs from 26.0 and 26.1 within a study.
  • FLAIR runs are processed by default when a dataset has them. Pass -m T1w T2w bold dwi to keep the 26.0 selection.
  • Anatomical runs with more than one volume are dropped with a warning. The check never applied to T1w and T2w before (#1474).
  • A BIDS database written by an earlier version keeps its old index, without the top-level sidecars: pass --bids-database-wipe when rerunning into an existing output folder (#1471).
  • The abide2bids command is removed (it had failed on import since 24.0). The usage guide now has a table of where each ABIDE subject lives in DataLad's ///abide (#1470).

Changes

Author list for papers based on MRIQC 26.1 series

As described in the Contributor Guidelines, anyone listed as a developer or contributor may write and submit manuscripts about MRIQC. To do so, please move the author(s) name(s) to the front of the following list:

Christopher J. Markiewicz 1; Zvi Baratz 2; Céline Provins 3; Eilidh MacNicol 4; Dimitri Papadopoulos Orfanos 5; Teresa Gomez 6; Dylan Nielson 7; Jan Varada 8; Ross W. Blair 1; McKenzie P. Hagen 9; William Triplett 10; Jon Haitz Legarreta Gorroño 11; Mathias Goncalves 1; Nikita Beliy 12; John A. Lee 13; Patrick Sadil 14; Ursula A. Tooley 15; Yaroslav O. Halchenko 16; Yibei Chen 17; James D. Kent 18; Bennet Fauber 19; Taylor Salo 20; Michael Krause 21; Pablo Velasco 22; Thomas Nichols 23; Victor Férat 24; Adam Huffman 25; Elodie Savary 3; Johannes Achtzehn 26; Joke Durnez 1; Satrajit S. Ghosh 27; Adam C. Raikes 28; Asier Erramuzpe 29; Benjamin Kay 30; Daniel Birman 1; Michael Dayan 31; Michael G. Clark 32; Rafael Garcia-Dias 33; Adam G. Thomas 34; Russell A. Poldrack 1; Ariel Rokem 6; Oscar Esteban 35.

Affiliations:

  1. Department of Psychology, Stanford University, CA, USA
  2. Quantivly Inc., Somerville, MA, USA
  3. Department of Radiology, Lausanne University Hospital and University of Lausanne, Switzerland
  4. Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
  5. NeuroSpin, CEA, Université Paris-Saclay, NeuroSpin, Gif-sur-Yvette, France
  6. The University of Washington eScience Institute, WA, USA
  7. Section on Clinical and Computational Psychiatry, National Institute of Mental Health, Bethesda, MD, USA
  8. Functional MRI Facility, National Institute of Mental Health, Bethesda, MD, USA
  9. Psychology Department, University of Washington, Seattle, WA, USA
  10. University of Florida: Gainesville, Florida, US
  11. Brigham and Women's Hospital, Mass General Brigham, Harvard Medical School, MA, USA
  12. CRC ULiege, Liege, Belgium
  13. Quansight, Dublin, Ireland
  14. Johns Hopkins Bloomberg School of Public Health, MD, USA
  15. Department of Neuroscience, University of Pennsylvania, PA, USA
  16. Psychological and Brain Sciences Department, Dartmouth College, NH, USA
  17. McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, USA
  18. Department of Psychology, University of Texas at Austin, TX, USA
  19. University of Michigan, Ann Arbor, USA
  20. Department of Psychology, Florida International University, FL, USA
  21. Max Planck Institute for Human Development, Berlin, Germany
  22. Center for Brain Imaging, New York University, NY, USA
  23. Oxford Big Data Institute, University of Oxford, Oxford, GB
  24. Department of Basic Neurosciences, Université de Genève, Geneva, Switzerland
  25. Department of Physics, Imperial College London, London, UK
  26. Charité Berlin, Berlin, Germany
  27. McGovern Institute for Brain Research, MIT, MA, USA; and Department of Otolaryngology, Harvard Medical School, MA, USA
  28. Center for Innovation in Brain Science, University of Arizona, Tucson, AZ, USA
  29. Computational Neuroimaging Lab, BioCruces Health Research Institute
  30. Washington University School of Medicine, St.Louis, MO, USA
  31. International Committee of the Red Cross - ICRC, Geneva, Switzerland
  32. National Institutes of Health, USA
  33. Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
  34. Data Science and Sharing Team, National Institute of Mental Health, Bethesda, MD, USA
  35. School of Engineering, HES-SO Valais/Wallis, Sion, Switzerland

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